President Rodrigo Duterte ratcheted up his feud with the United States on Monday, ordering all American special forces out of the southern Philippines where they have been advising local troops battling Muslim extremists.

Duterte's order came a week after he called US President Barack Obama "a son of a whore", causing Obama to cancel their scheduled bilateral meeting at a summit in Laos.

The Filipino leader, the first to hail from the south and who claims Muslim ancestry, has been stepping up efforts to bring peace to the southern Philippines, where decades-long insurgencies with Muslim and communist rebels have claimed more than 150,000 lives.

Last month he restarted peace talks with the largest separatist group, the 12,000-strong Moro Islamic Liberation Front (MILF), which like others has been fighting since the 1970s for an independent Islamic state or autonomous rule.

US advisors in the area help train Filipino troops but are barred from engaging in combat except in self-defence.

Previously, about 500-600 US personnel rotated through the Mindanao region but in 2014, then-defence secretary Voltaire Gazmin said this would be cut back to 200.

Duterte did not specify when or how many Americans would be expelled but said the Philippines alignment with the West was at the root of the persistent Muslim insurgency.

"These US special forces, they have to go in Mindanao," he told a gathering of government employees.

"The (Muslim) people will become more agitated. If they see an American, they will really kill him."

The Pentagon said it was aware of Duterte's statements but had not been contacted by authorities on the issue.

"We will continue to consult closely with our Filipino partners to appropriately tailor our assistance to whatever approach the new Administration adopts," Pentagon spokesman Gary Ross said.

The United States is Manila's main military ally and the Philippines' colonial ruler until 1946. In his speech, Duterte showed photographs and cited accounts of how US troops killed Muslims during America's occupation of the Philippines in the early-1900s to explain his decision.

Duterte's spokesman Ernesto Abella said that "the statement reflects (President Duterte's) new direction towards coursing an independent foreign policy".

The Filipino leader also hit out at Obama and UN Secretary-General Ban Ki-moon for criticising his bloody crackdown on crime that has claimed 3,000 lives in a little over two months.

"This Obama, when you accuse me of killing... let he who is without sin, cast the first stone," he said.

In a brief encounter in Laos, Obama urged the Filipino leader to conduct his war on crime "the right way" and protect human rights, but Duterte has said it is none of America's business.